How I beat the second year blues

I’m not sure why, but I thought I would never suffer from the second year PhD blues. Despite it taking me about two years of work (including part of my MRes) to get decent results, I remained positive. Last November, I started to get particularly exciting results and it laid out a clear path to the end of my doctorate.

But a few months ago, my reactions stopped working. Endless repeat reactions and tweaks were unsuccessful; I wanted to quit. The second year blues had found me and hit me hard.

In the last few weeks I’ve managed to get everything back on track. In fact the failed reactions might have shed some light on why the reaction works so well in the first place.

For anyone else in a similar position, I think it’s most important to stay motivated. I adopted a strategy of working on my main project and easier side projects on alternate days.

I think this has several benefits. By breaking up the disappointing results with easier work, I feel happier. Dealing with negative results for weeks on end was too much for me to handle.

I maintain momentum with side projects—something I struggled with before. I see side projects as backup publications, in case my main project goes down the drain. The time I spend not thinking about the main project helps me approach it with a fresh perspective too.

I find it helpful to tell people, like my supervisor and friends, whether I’m having a “main project day” or “side project day”. This stops me taking a risk of two consecutive days on the same project.

I recommend this strategy to any struggling students. There’s no point in slogging along, miserable. At least until I submit my thesis, it’s how I will work.

No funding, no placement

Today the Social Mobility and Child Poverty Commission published Elitist Britain?, a report on social mobility in the UK. The conclusions aren’t surprising. Numerous outlets have covered it (e.g. BBC, Guardian).

Careers in the media, politics and law are often singled out as being tough to crack unless you’re from a privileged background. What about science? A search for “science” in the report returns zero hits. It’s interesting that it’s not mentioned.

Every summer, departments at Imperial host students on the Undergraduate Research Opportunities Programme, my department included. I’m sure other universities run similar things. There are bursaries for living costs but competition is tough. In roughly five years I’ve yet to come across a recipient. So really they are unpaid internships, no different to those that are criticised in industries like the press or fashion. Only the offspring of the rich can afford to work for free, especially in London.

In 2009 I applied for a college bursary but I was unsuccessful. I thought it was game over, as I worked full time every holiday to pay off debts that accumulated during term time (when I only worked part time). But the principal investigator generously paid me to do the project anyway, for which I’m still very grateful. I think this is quite rare.

If I had not completed the placement would I have been accepted onto my fully-funded PhD programme? I don’t know. Is it fair that only the wealthiest students can afford to undertake placements and gain valuable research experience? No. If I were a PI, I would not employ unpaid students in my lab, even though I’d be losing out on free labour. Considering the gulf between the richest and poorest and lack of social mobility in the UK, I think a policy of “no funding, no placement” is well overdue.

Correcting the literature

Mathias Brust in Chemistry World:

Ideally, science ought to be self-correcting. … In general, once a new phenomenon has been described in print, it is almost never challenged unless contradicting direct experimental evidence is produced. Thus, it is almost certain that a substantial body of less topical but equally false material remains archived in the scientific literature, some of it perhaps forever.

Philip Moriarty expresses similar concern in a post at Physics Focus. Openly criticising other scientists’ work is generally frowned upon—flaws in the literature are “someone else’s problem”. Erroneous papers sit in the scientific record, accumulating a few citations. Moriarty thinks this is a problem because bibliometrics are (unfortunately) used to assess the performance of scientists.

I think this is a problem too, although for a different reason. During my MRes I wasted a lot of time trying to replicate a nanoparticle synthesis that I’m now convinced is totally wrong. Published in June 2011, it now has five citations according to Web of Knowledge. I blogged about it and asked what I should do. The overall response was to email the authors but in the end I didn’t bother. I wanted to cut my losses and move on. But it still really bugs me that other people could be wasting their limited time and money trying to repeat it when all along it’s (probably) total crap.

I did take my commenters’ advice and email an author about another reaction that has turned out to be a “bit of an art”. (Pro tip: if someone tells you a procedure is a bit of an art, find a different procedure.) I asked some questions about a particular procedure and quoted a couple of contradictions in their papers, asking for clarification/correction. His responses were unhelpful and after a couple of exchanges he stopped replying. Unlike the first case, I don’t believe the results are flat out wrong. Instead I suspect a few experimental details are missing or they don’t really know what happens. I think I’ll get to the bottom of it eventually, but it’s frustrating.

What are your options if you can’t replicate something or think it’s wrong? I can think of four (excluding doing nothing):

  1. Email the corresponding author. They don’t have an incentive to take it seriously. You are ignored.

  2. Email the journal editor. Again, unless they’re receiving a lot of emails, what incentive does the journal have to take it seriously? I suspect you’d be referred to the authors.

  3. Try and publish a rebuttal. Can you imagine the amount of work this would entail? Last time I checked, research proposals don’t get funded to disprove papers. This is only really a viable option if it’s something huge, e.g. arsenic life.

  4. Take to the Internet. Scientists, being irritatingly conservative, think you’re crazy. Potentially career damaging.

With these options, science is hardly self-correcting. I’d like to see a fifth: a proper mechanism for post-publication review. Somewhere it’s academically acceptable to ask questions and present counter results. I think discussion should be public (otherwise authors have little incentive to be involved) and comments signed (to discourage people from writing total nonsense). Publishers could easily integrate such a system into their web sites.

Do you think this would work? Would you use it? This does raise another question: should science try and be self-correcting at all?

Thanks to Adrian for bringing Mathias Brust’s article to my attention.

Routine operations

On Friday I went to a talk by Steven Ley titled Going with the Flow: Enabling Technologies for Molecule Makers. His group at Cambridge have done a lot of impressive work on flow chemistry over many years, both developing the technology and using it to synthesise organic molecules.

He covered a lot of ground in the talk, but one of his main points was that it is “unsustainable to use people for routine operations”. Chemists train for 10 years to then stand in front of a fume hood running columns. Ley wants to develop tools that allow researchers to make better use of their time in the laboratory. Flow chemistry has many benefits over batch chemistry, one of them being that it is easy to automate.

His talk left me wondering where I’m particularly inefficient in the lab. Sample collection and recording absorption spectra are particularly time consuming. Last year I started to build an (Arduino-powered) automatic sample collector, but made it far too complicated and never finished it. Now I’ve drastically simplified it (to the design my supervisor said I should use in the first place, as he often likes to remind me) and hope to have it working by the end of next week. I reckon it could save me anywhere between 5–10 hours a week of standing around swapping vials. I’m also going to make a start on recording absorption spectra inline. Again, this will save me a few hours a week, leaving me to do something more valuable.

I completely agree with Ley about the benefits of flow chemistry, but you can’t ignore that all this equipment costs money. Ley’s group use a lot of commercially available equipment and it’s not cheap. In my group, we build a lot of apparatus ourselves because we can tailor it to our needs and it’s a lot more “hackable” (as well as cheaper).

Someone in the audience tried to make the point during questions that funding is tight, especially for those working in organic synthesis. How they meant to afford equipment like £40,000 inline infrared spectrometers? Ley didn’t really answer this question (and I’m not sure he can). He’s obviously very well funded so he can build and develop the “lab of the future“.[^1] A lot of this technology might be out of the budget of the chemists who will benefit from it the most. Unfortunately they might be performing “routine operations” for some time to come.

[^1]: M.D. Hopkin, I.R. Baxendale, S.V. Ley, Chim. Oggi./Chemistry Today, 2011, 29, 28-32.

Details matter

Blog Syn is a new chemistry blog where chemists post their attempts to reproduce reactions from the literature. Each post starts with the following disclaimer:

The following experiments do not constitute rigorous peer review, but rather illustrate typical yields obtained and observations gleaned by trained synthetic chemists attempting to reproduce literature procedures…

I disagree completely. What could be more rigorous than actually trying a reaction?

So far there are three posts. The first gave a lower yield than reported. The second was “moderately reproducible”. The paper omitted details essential to the reaction’s success. The third was “difficult to reproduce” and is well worth reading—there’s a great response from one of the authors, Prof. Phil Baran.

It’s unacceptable for anyone to publish a paper without all the information necessary to replicate the results. It wastes researchers’ time and money. I’ve written before about my difficulties trying to replicate results. It’s infuriating. How do papers like this slip through peer review?

I suspect some authors don’t really know why a reaction gives a particular product, especially in nanoparticle synthesis. They manage to pull something off a few times and publish their findings, but (unknowingly) neglect parameters crucial for other researchers to be able to reproduce it. It could be something seemingly trivial, like the method used to wash the glassware. The next researcher does it differently because it’s not mentioned in the paper and gets a different result.

The only way to deal with this is for reviewers to demand thorough experimental sections. (But to do so they must have a good understanding of typical experimental procedures. This is a problem if your reviewer hasn’t been in the lab for years.)

An alternative scenario could be that the researchers, in the early stages of the work, find that doing X doesn’t work. Later they find doing Y does work. Y gets published. X stays in the laboratory notebook.

X is a negative result. On it’s own, it’s not very useful. Loads of attempted reactions don’t work. But in the context of the positive result (i.e. the paper) the negative result is actually very valuable to anyone who wants to repeat the paper. Serious consideration should be given to including them in the supplementary information.

Experimental methods are grossly oversimplified. We like things to be elegant and simple, but chemistry is complicated. There’s no excuse not to include more information because everything is published online and space constraints aren’t a problem.

Blog Syn shows that subtleties in chemistry are important. We should all acknowledge that in our own papers and demand that others do the same.

Tools and technologies for researchers

The Library at Imperial run a course called Blogs, Twitter, wikis and other web-based tools. They asked me (and also Jon Tennant) to give a quick talk to the attendees yesterday on the things I use to do my work.

Rather than give a slide-based presentation I decided the best thing to do was give a demo. I quite like mind mapping to help me structure ideas so I made one for this. I’ve included links to web sites where appropriate. You can download a PDF of the mind map here (PDF).

It’s split into two halves: the tools that I do use, categorised into “inputs” (e.g. Twitter and RSS) and “outputs” (e.g. Google Drive), and those that I don’t with some short reasons why. If you’re interested in trying some of this out, give one or two a go and see if you find them useful. If you use something that I haven’t mentioned, let me know in the comments.

Microwave heating: still nothing special

For many years there has been debate over whether there is a specific microwave effect on chemical reactions or if it’s just a thermal effect. A couple of years ago I took lecture course on microwave and ultrasound chemistry. The course covered a few papers on the existence of a microwave effect and concluded that there isn’t anything special going on—microwaves just give very efficient and fast heating compared to normal convective heating in an oil bath or dry-syn block.

I found course particularly interesting, so whenever I see a paper on the subject I at least read the abstract to see if anything has changed. Angewandte Chemie have recently published a paper titled Microwave Effects in Organic Synthesis—Myth or Reality? (DOI: 10.1002/anie.201204103) by C. Oliver Kappe, Bartholomäus Pieber, and Doris Dallinger.

They looked at two recently published papers that allegedly found a specific microwave effect. Both claimed microwave irradiation significantly enhanced the reaction rate or yield in a way that couldn’t be replicated by regular heating to the same temperature.

Summarising a few pages: Kappe et al. couldn’t replicate the findings and argue that the problem lies in poor temperature management. To test the existence of a specific (non-thermal) microwave effect you need to run the same reaction twice at the same temperature, one with microwaves and the other normally (e.g. with an oil bath).

However the researchers who report a microwave effect use external infrared temperature probes, which record a lower temperature than the bulk reaction mixture. Microwaves heat more efficiently than the normal heating, so the microwave reaction will give you a higher yield and both vessels are in fact not at the same temperature. Instead you must use fibre optic temperature probes placed inside the reaction vessels. Doing this eliminates any microwave specific effect. To quote:

Importantly, we firmly believe that the existence of genuine nonthermal microwave effects is a myth, as all our attempts to verify these often claimed “magical” microwave effects during the past decade have failed.

It’s a good read and, I think, a nice example of science at its best. I’m also glad I read it because a colleague and I had, for some reason, been looking at getting a microwave flow reactor—which would be completely pointless, as all the benefits of microwaves in batch chemistry (high pressures and homogeneous heating) can be readily achieved in flow using normal convective heating. If anyone could tell me why such an apparently pointless bit of kit exists, I’d like to know…

Reference: C.O. Kappe, B. Pieber and D. Dallinger, Microwave Effects in Organic Synthesis—Myth or Reality?, Angewandte Chemie International Edition, 2012. DOI:

Chem Coach Carnival

Here’s my very late contribution to See Arr Oh’s Chem Coach Carnival. The hashtag is #ChemCoach on Twitter.

Your current job.

I’m a PhD student at the Centre for Plastic Electronics at Imperial College London. I make metal nanoparticles of various shapes and sizes using flow reactors. Other researchers want them for use in organic electronic devices.

What you do in a standard “work day.”

Upon arriving at uni I immediately go for a shower because I cycle rather than take the tube. Riding my bike keeps me sane. Next thing: coffee.

After that I sit down and plan my day, most of which is spent in the lab. For my own research that involves analysing data, planning/doing reactions, ordering supplies/equipment, programming, building home-made equipment, doing electron microscopy, writing…

My work is very varied and I like it like that. I’m in a small group so everyone has to muck in and learn how to do lots of different things. Nothing is simply delegated to someone else. I think my work probably borders on chemical engineering/process chemistry.

I spent most of Friday running some preliminary tests on a new flow reactor. I also took delivery of a new optical microscope, then helped get rid of an old server rack because we’ve recently got a new optics table and need to make some space. After clearing up the mess I made in the lab I helped out our undergrad student with some MATLAB code.

I also spend one afternoon a week demonstrating for third year undergraduate physical chemistry labs. Teaching is fun, but sometimes very frustrating.

What kind of schooling/training/experience helped you get there?

I went to a comprehensive state school and sixth form before to Imperial for my undergraduate chemistry degree, where I’m now doing my PhD.

During my undergrad I did a summer placement with another group at Imperial, very generously funded by the supervisor. That confirmed for me that I wanted to do a PhD. I strongly recommend that students interested in a PhD do a summer placement.

I’ve also had a lot of non-chemistry part time jobs, mostly in bookshops. I’d like to think that’s given me a good try-anything, get-on-with-it attitude.

How does chemistry inform your work?

It doesn’t so much inform my work as form the core of it. It’s no good if I build the finest flow reactor in the world but my reaction doesn’t work.

I love running reactions, especially anything with a nice colour change. It’s so exciting when it works (and totally makes up for all the times it doesn’t). This Abstruse Goose comic sums up my feelings perfectly.

Finally, a unique, interesting, or funny anecdote about your career.

Not funny, but I’m fairly sure I’m the only person to have ever modified an Argos mini oven to make silver nanoparticles.

Conference talks: generally a bit rubbish?

Athene Donald recently wrote about what you don’t see at academic conferences. Academics may go to conferences in exotic places but they only see the inside of conference centres, hotels, airports and restaurants.

In the last year I’ve only been to two conferences. Unfortunately neither of them were in exotic places. The first was in York and I went with a few people from my group. As none of us are especially well-known in our field we unlike Athene had the freedom to explore York in the evenings. The second was held at Imperial and attendance was compulsory for DTC students. They were both small (no parallel talks) and lasted two days.

The speakers at both conferences, with the exception of one or two each day, were incredibly uninspiring and unenthusiastic. I remember trying to fall asleep one afternoon in York after nearly exhausting my iPhone battery reading papers. I was very disappointed as I had hoped to come back with fresh ideas but instead felt that it was a massive waste of time and money.

How can people talk so blandly about their own work? If the speaker isn’t excited by it then they most certainly can’t expect the audience to be interested. Many talks didn’t have any questions—the presentation equivalent of a death knell.

How have we ended up in this situation? I find it particularly baffling when I think about talks given by PhD students in my DTC. Recently we had a day with industry sponsors and visitors from other universities to listen to some third and final year PhD students present their work. The presentations were largely fantastic. Enthusiastic, confident, engaging, interesting… Really very good. Last month my cohort gave our MRes talks and the comments from markers were (nearly) all positive too. A world apart from the dreary, mind numbing talks I’ve sat through at my last two conferences.

Perhaps I’m overreacting, but I’ve really been put off going to anything other than something massive like the MRS conference where there will always be something related to my field and hence tolerable, even if the speaker is a bit tedious.

Does anyone else find most talks bad too? Are good talks unfortunately the exception? On the positive side, at least I’m at the beginning of my career so I can follow Athene’s advice, especially for my next trip to Italy in April:

Early career researchers, don’t kid yourself your professors enjoy themselves on such trips by seeing all the sights of the world you’ve always wanted to see yourself. Chances are, if you get to visit some far-flung place for a conference, you will enjoy your trip much more than your seniors because you live your life at a more leisurely pace. Make the most of it!

Open Access: Going for Gold?

Tonight the Science Communication Forum at Imperial College held a debate called Open Access: Going for Gold? with Stephen Curry (Imperial) and Mark Thorley (NERC, RCUK). The debate was chaired by Richard Van Noorden (Nature News).

Update 2 (28th September): you can listen to the debate on Figshare and here’s a useful link to RCUK’s open access policy (PDF).

Lots of things were discussed but a couple things in particular stuck in my mind writing this on the way home.

RCUK require for CC-BY for gold, but only CC-BY-NC for green

Under the new RCUK policy researchers must either pay a fee to publish in a gold open access journal or alternatively publish in a closed access journal and then deposit the article in a repository within 6 months.[^embargos]

Gold articles must be published with a CC-BY licence. This is good as it means anyone can do what they want with the work as long as the original authors are attributed. However, green articles deposited in a repository after the embargo period are only required to have a CC-BY-NC licence, meaning that you cannot use the work for commercial purposes.

This is very disappointing. Sadly it wasn’t discussed in the debate. CC-BY-NC is, as tweeted during the debate, a licence of fear. All it says is that the authors couldn’t think of a way to make money out of the work, so they’ll be damned if anyone else does. The work might as well have never happened.

Thorley talked about open access benefiting “UK PLC”, but CC-BY-NC is at complete odds with this. CC-BY-NC stifles innovation and progress. Furthermore, if the state funded the research, then the state and the rest of society should benefit from it. Under CC-BY-NC, no one benefits.

Green is of poorer quality than gold?

A couple of people doubted the quality of papers published straight to repositories like arXiv. I’m not so convinced. Firstly, they assume the reader is stupid and can’t work out for themselves if a paper is a load of nonsense. Secondly, it assumes that peer review weeds out all the bad papers. It doesn’t. Someone suggested a kitemark to say that a particular paper in a repository is trustworthy. I hope I don’t have to explain why that’s an awful idea.

Thorley did at one point say something about gold papers being better for the lay person. Curry looked quite suprised. This is a completely different debate. Just because a paper is literally accessible to the public doesn’t mean the information contained within it is intelligible to the public. But if someone is interested enough to be reading papers I don’t think gold/green will really make that much of a difference to them—not enough to justify an APC. I wonder what percentage of papers even undergo any major revisions between submission and publication.

Concluding thoughts

CC-BY-NC for green is a real disaster. I sincerely hope RCUK revise their policy so that it’s the same as gold.

I still can’t make up my mind about green versus gold. On the one hand, I think everything should go straight into repositories like arXiv. Forget journals and use the money we save to help fund and develop repositories, (although I know this is really very unlikely to ever happen). But on the other, if we are going to pay journals to publish work, we should expect more in return. Not just PDFs, but high quality (interactive?) documents including data and code in reuseable formats and tools to help us do things like text mining. I can’t help but think there’s very little innovation in publishing, especially considering the size of their profit margins.

It’s clear a lot more will happen in the open access debate. As Thorley said, this isn’t an event, it’s a journey. Hopefully it won’t be too arduous.

Update: gold—a free market for innovation?

Having slept it on it I can see where RCUK are coming from with their preference for gold, but I think they’re overestimating what publishers actually offer at the moment. Do most journals currently add enough value for it to be worth the APC? I’m not sure. I get the feeling people tend to think that every journal produces papers as beautiful as NPG. Authors will be paying the journal to publish, therefore we should expect more in return—especially considering the tidy profit margins. At present, I don’t think gold is that much better than green in that respect.

If, as Curry said, scientists end their addiction to impact factors (increasingly likely as HEFCE will be enforcing their ban on them), gold might lead to a more free market-like situation. Scientists will look around for journals that offer the best value for money. This could really drive innovation in scientific publishing as publishers are going to be competing in terms of what they can offer scientists rather than what the journal can do for an author’s career.

(Updated on 09:02 on 27th September 2012 with additional section.)

[^embargos]: Thorley said that the embargo periods vary in length from publisher to publisher. He was pretty clear about 6 months and said 12 months was “a joke”. Personally I think 6 months is still far too long. It also raises the question: do publishers only add such little value that its only worth 6 months? Why bother with it in the first place?